I just watched all four movies again. And I got a theory about the "Aliens" from The Kingdom of the Crystal Skull.

Also, spoilers for those who haven't played Fate of Atlantis.

Now, suppose some Atlanteans succeeded in making themselves "gods", what if this is what happened to the Aliens in Akator, that they were actually Atlantean kings, who transformed themselves and migrated to South America.
Then they expanded their technology even further and discovered a way to another dimension.
I think the Alien's anatomy is way too human to be being FROM another dimension, so I think it's more logical that they were human in the beginning, and changed, their bones turned to crystal and some other aspected changed aswell.
This also fits with Tikal featuring in Fate of Atlantis.